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HLCS Gene

protein-coding   GIFtS: 63
GCID: GC21M038123

Holocarboxylase Synthetase (Biotin-(Proprionyl-CoA-Carboxylase...

(Previous names: holocarboxylase synthetase (biotin-[proprionyl-Coenzyme...)
  See HLCS-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, 15RNAdb, and/or 11Nature:405,311-319 and CroW21)
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Aliases
Holocarboxylase Synthetase (Biotin-(Proprionyl-CoA-Carboxylase
(ATP-Hydrolysing)) Ligase)1 2
     Biotin--[Acetyl-CoA-Carboxylase] Ligase2
Holocarboxylase Synthetase (Biotin-(Proprionyl-Coenzyme A-Carboxylase
(ATP-Hydrolysing)) Ligase)1 2
     Biotin--[Methylcrotonoyl-CoA-Carboxylase] Ligase2
Biotin Apo-Protein Ligase2 3     Biotin--[Methylmalonyl-CoA-Carboxytransferase] Ligase2
HCS2 5     Biotin--Protein Ligase2
Holocarboxylase Synthetase (Biotin-[Proprionyl-Coenzyme A-Carboxylase
(ATP-Hydrolysing)] Ligase)1
     EC 6.3.4.-3
Holocarboxylase Synthetase, EC 6.3.411     

External Ids:    HGNC: 49761   Entrez Gene: 31412   Ensembl: ENSG000001592677   OMIM: 6090185   UniProtKB: P507473   

Export aliases for HLCS gene to outside databases

Previous GC identifers: GC21M034700 GC21M037043 GC21M037045 GC21M023599


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for HLCS Gene:
This gene encodes an enzyme that catalyzes the binding of biotin to carboxylases and histones. The protein plays
an important role in gluconeogenesis, fatty acid synthesis and branched chain amino acid catabolism. Defects in
this gene are the cause of holocarboxylase synthetase deficiency. Multiple alternatively spliced variants,
encoding the same protein, have been identified.(provided by RefSeq, Jun 2011)

GeneCards Summary for HLCS Gene:
HLCS (holocarboxylase synthetase (biotin-(proprionyl-CoA-carboxylase (ATP-hydrolysing)) ligase)) is a protein-coding gene. Diseases associated with HLCS include holocarboxylase synthetase deficiency, and biotinidase deficiency. GO annotations related to this gene include biotin binding and protein homodimerization activity.

UniProtKB/Swiss-Prot: BPL1_HUMAN, P50747
Function: Post-translational modification of specific protein by attachment of biotin. Acts on various
carboxylases such as acetyl-CoA-carboxylase, pyruvate carboxylase, propionyl CoA carboxylase, and
3-methylcrotonyl CoA carboxylase




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics, Whole Chromsome Sequence According to Nature (Cited Here with Permission):405,311-319 and CroW21)
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RefSeq DNA sequence at NCBI GenBank:
NC_000021.8  NT_011512.12  NC_018932.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the HLCS gene promoter:
         TBP   MAZR   FOXF2   NF-kappaB   E4BP4   RORalpha1   FOXJ2 (long isoform)   FOXJ2   NF-kappaB1   Pax-4a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): HLCS promoter sequence

   Search Chromatin IP Primers for HLCS

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HLCS


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 21q22.13   Ensembl cytogenetic band:  21q22.13   HGNC cytogenetic band: 21q22.1
Nature(405: 311-319) cytogenetic band:   21q22.13
HLCS Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HLCS gene location
GeneLoc information about chromosome 21         GeneLoc Exon Structure

(about GC identifiers)
GC21M038123:   GeneLoc Nature:405,311-319
Start:
38,123,189 bp from pter       23,699,922 bp from centromere
End:
38,362,545 bp from pter 23,910,899 bp from centromere
Size:
239,357 bases 210,978 bases
Orientation:
minus strand minus strand

Whole chromosome sequencing:
cDNA sequence: D87328
genomic clones: KB594G10 to pD47


(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: BPL1_HUMAN, P50747 (See protein sequence)
Recommended Name: Biotin--protein ligase  
Size: 726 amino acids; 80760 Da
Subunit: Monomer
Secondary accessions: D3DSG6 Q99451

Explore the universe of human proteins at neXtProt for HLCS: NX_P50747

Explore proteomics data for HLCS at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See HLCS Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (3 alternative transcripts): 
    NP_000402.3  NP_001229713.1  NP_001229714.1  

    ENSEMBL proteins: 
     ENSP00000338387   ENSP00000382071   ENSP00000392923   ENSP00000396370   ENSP00000396443  
    Reactome Protein details: P50747

    HLCS Human Recombinant Protein Products:

    Browse Purified and Recombinant Proteins at EMD Millipore
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    Browse recombinant and purified proteins available from Enzo Life Sciences
    OriGene Purified Protein for HLCS
    OriGene Protein Over-expression Lysate for HLCS
    OriGene MassSpec for HLCS
    OriGene Custom Protein Services for HLCS
    GenScript Custom Purified and Recombinant Proteins Services for HLCS
    Novus Biologicals HLCS Proteins
    Novus Biologicals HLCS Lysates
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for HLCS

     
    Search eBioscience for Proteins for HLCS 

    HLCS Antibody Products:

    Browse EMD Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Browse R&D Systems for Antibodies
    OriGene Antibodies for HLCS
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    Novus Biologicals HLCS Antibodies
    Abcam antibodies for HLCS
    Cloud-Clone Corp. Antibodies for HLCS
    ThermoFisher Antibodies for HLCS
    LSBio Antibodies in human, mouse, rat for HLCS

    HLCS Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    Browse R&D Systems for biochemical assays
    GenScript Custom Assay Services for HLCS
    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for HLCS
    Cloud-Clone Corp. CLIAs for HLCS
    Search eBioscience for ELISAs for HLCS 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    3 InterPro protein domains:
     IPR003142 BPL_C
     IPR004408 Biotin_CoA_COase_ligase
     IPR004143 BPL_LipA_LipB

    Graphical View of Domain Structure for InterPro Entry P50747

    ProtoNet protein and cluster: P50747

    1 Blocks protein domain: IPB003142 Biotin protein ligase

    UniProtKB/Swiss-Prot: BPL1_HUMAN, P50747
    Similarity: Belongs to the biotin--protein ligase family


    Find genes that share domains with HLCS           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: BPL1_HUMAN, P50747
    Function: Post-translational modification of specific protein by attachment of biotin. Acts on various
    carboxylases such as acetyl-CoA-carboxylase, pyruvate carboxylase, propionyl CoA carboxylase, and
    3-methylcrotonyl CoA carboxylase
    Catalytic activity: ATP + biotin + apo-[methylmalonyl-CoA:pyruvate carboxytransferase] = AMP + diphosphate +
    [methylmalonyl-CoA:pyruvate carboxytransferase]
    Catalytic activity: ATP + biotin + apo-[propionyl-CoA:carbon-dioxide ligase (ADP-forming)] = AMP + diphosphate +
    [propionyl-CoA:carbon-dioxide ligase (ADP-forming)]
    Catalytic activity: ATP + biotin + apo-[3-methylcrotonoyl-CoA:carbon-dioxide ligase (ADP-forming)] = AMP +
    diphosphate + [3-methylcrotonoyl-CoA:carbon-dioxide ligase (ADP-forming)]
    Catalytic activity: ATP + biotin + apo-[acetyl-CoA:carbon-dioxide ligase (ADP-forming)] = AMP + diphosphate +
    [acetyl-CoA:carbon-dioxide ligase (ADP-forming)]
    Biophysicochemical properties: Kinetic parameters: KM=224 nM for biotin; Vmax=143.9 pmol/min/mg enzyme;

         Genatlas biochemistry entry for HLCS:
    holocarboxylase synthetase,80kDa,cytosolic,with two alternatively spliced isoforms,catalyzing the biotinylation of
    the four biotin-dependent carboxylases,including the mitochondrial pyruvate carboxylase,propionyl-CoA
    carboxylase,methylcrotonyl-CoA carboxylase and the cytosolic acetyl-CoA carboxylase

         Enzyme Number (IUBMB): EC 6.3.4.-1

         Gene Ontology (GO): Selected molecular function terms (see all 11):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003824catalytic activity ----
    GO:0004077biotin-[acetyl-CoA-carboxylase] ligase activity IEA--
    GO:0004078biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity IEA--
    GO:0004079biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity IEA--
    GO:0004080biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity IDA7842009
         
    Find genes that share ontologies with HLCS           About GenesLikeMe


    Phenotypes:
         1 MGI phenotypic allele for Hlcs (no phenotypes)

    Find genes that share phenotypes with HLCS           About GenesLikeMe

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for HLCS
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for HLCS

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for HLCS
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for HLCS

    miRNA
    Products:
        
    Block miRNA regulation of human, mouse, rat HLCS using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate HLCS (see all 36):
    hsa-miR-411* hsa-miR-607 hsa-miR-4307 hsa-miR-379* hsa-miR-218-1* hsa-miR-766 hsa-miR-9 hsa-miR-2116
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for HLCS
    Predesigned siRNA for gene silencing in human, mouse, rat HLCS

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for HLCS

    Clone
    Products:
         
    OriGene clones in human, mouse for HLCS (see all 6)
    OriGene ORF clones in mouse, rat for HLCS
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: HLCS (NM_000411)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for HLCS
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HLCS

    Cell Line
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    Browse ESI BIO Cell Lines and PureStem Progenitors for HLCS 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HLCS


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    BPL1_HUMAN, P50747: Cytoplasm. Mitochondrion
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol5
    mitochondrion5
    nucleus5
    endoplasmic reticulum1
    peroxisome1

    Gene Ontology (GO): Selected cellular component terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000785chromatin IDA14613969
    GO:0005652nuclear lamina IDA14613969
    GO:0005737cytoplasm IDA--
    GO:0005739mitochondrion IEA--
    GO:0005829cytosol TAS--

    Find genes that share ontologies with HLCS           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for HLCS About    
    See pathways by source

    SuperPathSelected contained pathways About (see all per SuperPath)
    1Defective BTD causes biotidinase deficiency
    Defective BTD causes biotidinase deficiency1.00
    Metabolism of vitamins and cofactors1.00
    Defective AMN causes hereditary megaloblastic anemia 11.00
    Defective MMACHC causes methylmalonic aciduria and homocystinuria type cblC1.00
    Defective MMAA causes methylmalonic aciduria type cblA1.00
    Defective MUT causes methylmalonic aciduria mut type1.00
    Defective CD320 causes methylmalonic aciduria1.00
    Defects in cobalamin (B12) metabolism1.00
    2Metabolism
    Metabolism0.38
    Metabolic pathways0.38
    3Disease
    Disease
    4Biotin metabolism
    Biotin metabolism


    Find genes that share SuperPaths with HLCS           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 BioSystems Pathway for HLCS
        biotin-carboxyl carrier protein assembly

    1 Reactome Pathway for HLCS
        Biotin transport and metabolism


    2 Kegg Pathways  (Kegg details for HLCS):
        Biotin metabolism
    Metabolic pathways

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for HLCS
    Interactions:

        Search GeneGlobe Interaction Network for HLCS

    STRING Interaction Network Preview (showing 5 interactants - click image to see 16)

    Selected Interacting proteins for HLCS (P507471, 2, 3 ENSP000003383874) via UniProtKB, MINT, STRING, and/or I2D (see all 32)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ACACBO007631, 2, 3, ENSP000003670794EBI-3915568,EBI-2211739 MINT-7543053 MINT-7543129 MINT-7543070 MINT-7543096 I2D: score=2 STRING: ENSP00000367079
    NHP2L1P557693, ENSP000002159564I2D: score=3 STRING: ENSP00000215956
    UBCP0CG483, ENSP000003448184I2D: score=1 STRING: ENSP00000344818
    ADAP008133I2D: score=1 
    ATP5A1P257053I2D: score=1 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 10):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006464cellular protein modification process ----
    GO:0006766vitamin metabolic process TAS--
    GO:0006767water-soluble vitamin metabolic process TAS--
    GO:0006768biotin metabolic process TAS--
    GO:0008283cell proliferation IMP18429047

    Find genes that share ontologies with HLCS           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for HLCS (BPL1)

    6 HMDB Compounds for HLCS    About this table
    CompoundSynonyms CAS #PubMed Ids
    Adenosine monophosphate5'-AMP (see all 28)61-19-8--
    Adenosine triphosphate5'-(tetrahydrogen triphosphate) Adenosine (see all 24)56-65-5--
    Biotin(+)-Biotin (see all 42)58-85-5--
    Biotinyl-5'-AMP(+)-Biotinyl 5'-adenylate (see all 11)4130-20-5--
    Phosphoric acidacide phosphorique (FRENCH) (see all 20)7664-38-2--
    Pyrophosphate(4-)Diphosphoric acid ion (see all 10)14000-31-8--

    1 DrugBank Compound for HLCS    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    Biotin(+)-cis-Hexahydro-2-oxo-1H-thieno[3,4]imidazole-4-valeric acid (see all 7)58-85-5target--17056793 16772434 16359899

    Selected Novoseek inferred chemical compound relationships for HLCS gene (see all 17)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    biotin 93.9 311 17904341 (9), 19056636 (9), 10590022 (6), 19160459 (5) (see all 85)
    3-methylcrotonyl-coa 79.5 3 10770035 (1), 16398167 (1)
    multivitamin 67 2 20357078 (1), 15905112 (1)
    d-biotin 66.3 2 8814349 (1)
    acetyl-coa 63.6 8 11959985 (1), 20443544 (1), 10770035 (1), 19914215 (1) (see all 5)
    lysine 57.6 15 16772434 (1), 20026029 (1), 15992689 (1), 19369050 (1) (see all 7)
    pyruvate 45.9 3 16417669 (1), 10770035 (1)
    carnitine 34.1 6 16494802 (2), 17417720 (2), 8006369 (1), 7707691 (1)
    s-adenosylmethionine 26.5 1 17441947 (1)
    fatty acid 22.6 2 19740736 (1)



    Find genes that share compounds with HLCS           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for HLCS gene (3 alternative transcripts): 
    NM_000411.6  NM_001242784.1  NM_001242785.1  

    Unigene Cluster for HLCS:

    Holocarboxylase synthetase (biotin-(proprionyl-CoA-carboxylase (ATP-hydrolysing)) ligase)
    Hs.371350  [show with all ESTs]
    Unigene Representative Sequence: NM_001242784
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000336648(uc021wjb.1 uc002yvs.3) ENST00000399120(uc010gnb.3 uc010gnc.2)
    ENST00000482273 ENST00000448340 ENST00000419461 ENST00000427746
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate HLCS (see all 36):
    hsa-miR-411* hsa-miR-607 hsa-miR-4307 hsa-miR-379* hsa-miR-218-1* hsa-miR-766 hsa-miR-9 hsa-miR-2116
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat HLCS
    Clone
    Products:
         
    OriGene clones in human, mouse for HLCS (see all 6)
    OriGene ORF clones in mouse, rat for HLCS
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: HLCS (NM_000411)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for HLCS
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HLCS
    Primer
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    OriGene qPCR primer pairs and template standards for HLCS
    OriGene qSTAR qPCR primer pairs in human, mouse for HLCS
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat HLCS
      QuantiTect SYBR Green Assays in human, mouse, rat HLCS
      QuantiFast Probe-based Assays in human, mouse, rat HLCS

    Additional mRNA sequence: 

    AJ001864.1 AK307940.1 AK314189.1 BC060787.1 D23672.2 D87328.1 X80160.1 

    9 DOTS entries:

    DT.87016761  DT.95322534  DT.121130831  DT.97819961  DT.70101842  DT.95188497  DT.121130826  DT.435409 
    DT.92427566 

    Selected AceView cDNA sequences (see all 117):

    Z44722 F10644 AA450362 BE671228 AI753884 AL043777 AI951058 AW014529 
    BU542434 W17009 F10768 BF224167 NM_000411 AA993715 D23672 F13164 
    BQ717432 X80160 BE503952 AI753201 CA312137 CB529960 BM930024 F02586 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for HLCS (see all 15)    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3a · 3b · 3c · 3d ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10a · 10b · 10c · 10d · 10e · 10f · 10g · 10h ^ 11a ·
    SP1:              -     -     -     -     -     -     -     -                 -     -                                                                           
    SP2:                                                                                      -                                                                     
    SP3:                    -     -     -     -     -     -     -                 -     -                                                                           
    SP4:                                            -     -     -                 -     -                                                                           
    SP5:              -     -     -     -     -     -     -     -                       -     -                                                                     

    ExUns: 11b ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18a · 18b ^ 19 ^ 20
    SP1:              -     -     -                                   -         
    SP2:              -     -     -                                   -         
    SP3:                                                                        
    SP4:                                                                        
    SP5:                                                                        


    ECgene alternative splicing isoforms for HLCS

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    HLCS expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGAGAATCCT
    HLCS Expression
    About this image


    HLCS expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 5) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Ovary (Reproductive System)
             Oviduct
     
     Pancreas (Endocrine System)
             Islets of Langerhans
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
     
     Liver (Hepatobiliary System)
             Hepatocytes Liver Lobule
    HLCS Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    HLCS Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.371350

    UniProtKB/Swiss-Prot: BPL1_HUMAN, P50747
    Tissue specificity: Mostly expressed in muscle, placenta, in lesser extent in the brain, kidney, pancreas, liver
    and lung

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for HLCS gene from Selected species (see all 17)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Hlcs1 , 5 holocarboxylase synthetase (biotin- [propriony-Coenzyme more1, 5 78.59(n)1
    77.25(a)1
      16 (55.12 cM)5
    1109481  NM_139145.41  NP_631884.11 
     941293065 
    chicken
    (Gallus gallus)
    Aves HLCS1 holocarboxylase synthetase (biotin-(proprionyl-CoA-carboxylase more 64.57(n)
    61.12(a)
      418516  XM_004934539.1  XP_004934596.1 
    lizard
    (Anolis carolinensis)
    Reptilia HLCS6
    Uncharacterized protein
    60(a)
    1 ↔ 1
    3(141020365-141143345)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia hlcs1 holocarboxylase synthetase (biotin-(proprionyl-CoA-carboxylase more 60.84(n)
    56.94(a)
      100492512  XM_004912118.1  XP_004912175.1 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.120602 Transcribed sequence with weak similarity to protein more 71.88(n)    CD753666.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Hcs6
    Holocarboxylase synthetase
    16(a)
    1 ↔ 1
    3R(1300624-1311115)
    worm
    (Caenorhabditis elegans)
    Secernentea bpl-11 bpl-1 42.72(n)
    30.71(a)
      174039  NM_182120.4  NP_871920.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes BPL1(YDL141W)4 Biotin:apoprotein ligase, covalently modifies proteins more   --   4(203039-205111) 851414  NP_010140.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons HCS11 HCS1 46.01(n)
    34.22(a)
      817112  NM_128130.2  NP_565605.1 


    ENSEMBL Gene Tree for HLCS (if available)
    TreeFam Gene Tree for HLCS (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for HLCS (see all 5239)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 21 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs289346021,2,,4
    CHolocarboxylase synthetase deficiency (HLCS deficiency)4 pathogenic128856252(-) TCTGCG/TGTTGG 6 R L mis1 ese30--------
    VAR_0465164
    Holocarboxylase synthetase deficiency (HLCS deficiency)4--see VAR_0465162 D Y mis40--------
    VAR_0465154
    Holocarboxylase synthetase deficiency (HLCS deficiency)4--see VAR_0465152 D N mis40--------
    VAR_0130094
    Holocarboxylase synthetase deficiency (HLCS deficiency)4--see VAR_0130092 R W mis40--------
    VAR_0465134
    Holocarboxylase synthetase deficiency (HLCS deficiency)4--see VAR_0465132 V G mis40--------
    VAR_0465114
    Holocarboxylase synthetase deficiency (HLCS deficiency)4--see VAR_0465112 L S mis40--------
    VAR_0091984
    Holocarboxylase synthetase deficiency (HLCS deficiency)4--see VAR_0091982 V M mis40--------
    VAR_0091974
    Holocarboxylase synthetase deficiency (HLCS deficiency)4--see VAR_0091972 T I mis40--------
    VAR_0465094
    Holocarboxylase synthetase deficiency (HLCS deficiency)4--see VAR_0465092 V D mis40--------
    VAR_0091964
    Holocarboxylase synthetase deficiency (HLCS deficiency)4--see VAR_0091962 V E mis40--------

    HapMap Linkage Disequilibrium report for HLCS (38123189 - 38362545 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for HLCS (see all 11):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2676526CNV Deletion23128226
    esv2659201CNV Deletion23128226
    esv2666311CNV Deletion23128226
    nsv3508CNV Insertion18451855
    nsv510504CNV Loss20534489
    esv26519CNV Loss19812545
    nsv3507CNV Loss18451855
    nsv913735CNV Loss21882294
    nsv913736CNV Loss21882294
    nsv498978CNV Loss21111241

    Human Gene Mutation Database (HGMD): HLCS
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing HLCS
    DNA2.0 Custom Variant and Variant Library Synthesis for HLCS

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 609018   
    OMIM disorders: 253270  
    UniProtKB/Swiss-Prot: BPL1_HUMAN, P50747
  • Holocarboxylase synthetase deficiency (HLCS deficiency) [MIM:253270]: A neonatal form of multiple
    carboxylase deficiency, an autosomal recessive disorder of biotin metabolism, characterized by ketoacidosis,
    hyperammonemia, excretion of abnormal organic acid metabolites, and dermatitis. In holocarboxylase synthetase
    deficiency, clinical and biochemical symptoms improve dramatically with administration of biotin. Note=The
    disease is caused by mutations affecting the gene represented in this entry

  • 6 diseases for HLCS:    
    About MalaCards
    holocarboxylase synthetase deficiency    biotinidase deficiency    multiple carboxylase deficiency    propionic acidemia
    biotin deficiency    organic acidemia

    3 diseases from the University of Copenhagen DISEASES database for HLCS:
    Multiple carboxylase deficiency     Organic acidemia     Metabolic acidosis

    Find genes that share disorders with HLCS           About GenesLikeMe

    Selected Novoseek inferred disease relationships for HLCS gene (see all 16)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    holocarboxylase synthetase deficiency 99.1 54 9758715 (4), 16650223 (4), 8982946 (3), 16494802 (2) (see all 36)
    multiple carboxylase deficiency 98.7 39 8817339 (2), 18429047 (2), 2123277 (1), 9350481 (1) (see all 24)
    biotinidase deficiency 91.4 15 18845537 (2), 9492625 (2), 2123277 (1), 7825232 (1) (see all 11)
    aciduria organic 81.5 4 12633764 (1), 8541348 (1)
    metabolic acidosis 64.6 5 16650223 (1), 8541348 (1), 10234606 (1), 19695181 (1)
    propionic acidemia 58.2 1 16997619 (1)
    metabolic disorder 54.1 9 8319716 (1), 15095958 (1), 10770035 (1), 16494802 (1) (see all 6)
    methylmalonic aciduria 47.9 3 16997619 (1)
    ketosis 39.7 1 11196112 (1)
    ketoacidosis 37.5 3 10190325 (1), 10653324 (1)

    Genatlas disease: HLCS
    multiple carboxylase deficiency,early onset with feeding difficulties,hypotonia,seizures,lethargy and metabolic
    acidosis mild,hyperammonemia,organic aciduria

    Genetic Association Database (GAD): HLCS

    Export disorders for HLCS gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for HLCS gene, integrated from 10 sources (see all 154):
    (articles sorted by number of sources associating them with HLCS)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Isolation and characterization of mutations in the human holocarboxylase synthetase cDNA. (PubMed id 7842009)1, 2, 3, 9 Suzuki Y.... Narisawa K. (Nat. Genet. 1994)
    2. Structure of human holocarboxylase synthetase gene and mutation spectrum of holocarboxylase synthetase deficiency. (PubMed id 11735028)1, 2, 9 Yang X.... Suzuki Y. (Hum. Genet. 2001)
    3. Reduced half-life of holocarboxylase synthetase from patients with severe multiple carboxylase deficiency. (PubMed id 18429047)1, 2, 9 Bailey L.M....Polyak S.W. (Hum. Mutat. 2008)
    4. Characterization of mutant holocarboxylase synthetase (HCS): a Km for biotin was not elevated in a patient with HCS deficiency. (PubMed id 9396568)1, 2, 9 Aoki Y....Narisawa K. (Pediatr. Res. 1997)
    5. Clustering of mutations in the biotin-binding region of holocarboxylase synthetase in biotin-responsive multiple carboxylase deficiency. (PubMed id 8817339)1, 2, 9 Dupuis L.... Gravel R.A. (Hum. Mol. Genet. 1996)
    6. Molecular analysis of holocarboxylase synthetase deficiency: a missense mutation and a single base deletion are predominant in Japanese patients. (PubMed id 8541348)1, 2, 9 Aoki Y.... Narisawa K. (Biochim. Biophys. Acta 1995)
    7. Identification and characterization of mutations in patients with holocarboxylase synthetase deficiency. (PubMed id 10190325)1, 2, 9 Aoki Y.... Narisawa K. (Hum. Genet. 1999)
    8. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    9. Clinical findings and biochemical and molecular analysis of four patients with holocarboxylase synthetase deficiency. (PubMed id 12124727)1, 2 Morrone A.... Zammarchi E. (Am. J. Med. Genet. 2002)
    10. The DNA sequence of human chromosome 21. (PubMed id 10830953)1, 2 Hattori M.... Yaspo M.-L. (Nature 2000)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 3141 HGNC: 4976 AceView: HLCS Ensembl:ENSG00000159267 euGenes: HUgn3141
    ECgene: HLCS Kegg: 3141 H-InvDB: HLCS

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for HLCS Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=HLCS[genesymbol]

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for HLCS gene:
    Search GeneIP for patents involving HLCS

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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